Path includeInputs does not work for symlinks

[pditommaso]

Try

process foo {
  input:
    path x from '/some/data/foo.txt'
  output:
    path '*', includeInputs:true into foo_ch
  """
  touch file.txt
  """
}

foo_ch.view { "foo: $it.name" }

[mahesh-panchal]

But this works:

#! /usr/bin/env nextflow

nextflow.preview.dsl=2

workflow {

    TEST_PATH(Channel.fromPath('test_ref.fa'))
    TEST_PATH.out.view()

}

process TEST_PATH {

    scratch true

    input:
    path reference

    output:
    path ("${reference}*",includeInputs:true)
 
    script:
    """
    touch ${reference}.fai
    touch ${reference}.bwt
    """

}

So it's just a dsl1 issue?

[mahesh-panchal]

I think I misunderstood. The problem is if the file does not exist, then it's not included in the output with includeInputs:true, right?

[pditommaso]

I've seen happending when the input file is staged as symlink (default for shared hpc storage) the input file is not included even adding includeInputs:true

[mahesh-panchal]

Hmm. I'm not sure what to add to help. It's working for me on the HPC system I'm using and following symlinks. I'm also using process.scratch = '$SNIC_TMP', which evaluates to /scratch/<slurm_job_id>, singularity, nextflow v20.01.0, dsl2. cp is using cp (GNU coreutils) 8.22.

[pditommaso]

But for you it's fine, isn't it?

[mahesh-panchal]

Yes. It's working fine for me.

Symlinks are being followed on my HPC system.

[pditommaso]

Ok, I'll concentrate on my issue then :)

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[pditommaso]

keep open

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.